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Miscellaneous Functions from Alexey Shipunov
A collection of functions for data manipulation, plotting and statistical computing, to use separately or with the book "Visual Statistics. Use R!": Shipunov (2020) < http://ashipunov.info/shipunov/software/r/r-en.htm>. Dr Alexey Shipunov died in December 2022. Most useful functions: Bclust(), Jclust() and BootA() which bootstrap hierarchical clustering; Recode() which does multiple recoding in a fast, simple and flexible way; Misclass() which outputs confusion matrix even if classes are not concerted; Overlap() which measures group separation on any projection; Biarrows() which converts any scatterplot into biplot; and Pleiad() which is fast and flexible correlogram.
R Fortunes
A collection of fortunes from the R community.
Extending Nucleic Acid Melting Temperature Analysis from Sequence-Level Computation to Genome-Wide Thermodynamic Profiling
Accurate calculation of nucleic acid melting temperature (Tm) is fundamental to many molecular biology applications, and this software scales Tm analysis from individual sequences to genome‑wide thermodynamic profiling. This package extends Tm analysis from simple sequence level computation to comprehensive genome-wide thermodynamic profiling. It takes multiple input formats including sequence strings, FASTA files, genomic coordinates. The implementation provides three Tm calculation methods: the Wallace rule (Thein & Wallace, 1986), empirical GC‑content formulas (Marmur, 1962; Schildkraut, 2010; Wetmur, 1991; Untergasser, 2012; von Ahsen, 2001), and nearest‑neighbor thermodynamics (Breslauer, 1986; Sugimoto, 1996; Allawi, 1998; SantaLucia, 2004; Freier, 1986; Xia, 1998; Chen, 2012; Bommarito, 2000; Turner, 2010; Sugimoto, 1995; Allawi, 1997; SantaLucia, 2005). Corrections are supported for salt ions (SantaLucia, 1996, 1998; Owczarzy, 2004, 2008) and for chemical conditions such as dimethyl sulfoxide and formamide. This package returns result as a GRanges object for interoperability with Bioconductor workflows and downstream multi-omics analyses. Data-level integration reconciles Tm windows with external multi-omics GRanges objects through overlap, nearest-feature, windowed-count, and binned-average strategies, returning a single unified GRanges object ready for downstream analysis. Visualization-level integration renders multiple feature layers as independent concentric tracks on a shared genomic axis, each retaining its native coordinate resolution. Group comparison supports Wilcoxon rank-sum and Student's t-tests with multiple available correction methods for contrasting Tm and other features across region classes.
A Collection of Small Text Corpora of Interesting Data
A collection of small text corpora of interesting data. It contains all data sets from 'dariusk/corpora'. Some examples: names of animals: birds, dinosaurs, dogs; foods: beer categories, pizza toppings; geography: English towns, rivers, oceans; humans: authors, US presidents, occupations; science: elements, planets; words: adjectives, verbs, proverbs, US president quotes.
Lactation Curve Parameter Estimation
AllCurves() runs multiple lactation curve models and extracts selection criteria for each model.
This package summarises the most common lactation curve models from the last century and provides a tool
for researchers to quickly decide on which model fits their data best to proceed with their analysis.
Start parameters were optimized based on a dataset with 1.7 million Holstein-Friesian cows. If convergence fails,
the start parameters need to be manually adjusted.
The models included in the package are taken from:
(1) Michaelis-Menten: Michaelis, L. and M.L. Menten (1913).